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fRMA | Frozen robust multiarray analysis for Affymetrix Exon and Gene ST arrays

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A package based on a single-array preprocessing algorithm that retains the advantages of multiarray algorithms and removes certain batch effects by downweighting probes that have high between-batch residual variance. By using a large biologically diverse database of microarrays from a large number of different laboratories spanning several years, the fRMA algorithm is able to differentiate between outliers and probes that show a consistent susceptibility to batch effects. These batchy probes are downweighted during summarization to minimize their effect on expression estimates. The frmaTools package which allows users to create their own frozen parameter vectors, has also been updated to work with oligo GeneFeatureSet and ExonFeatureSet objects. This allows users to create custom vectors for the HuEx and HuGene platforms and to implement fRMA on other Affymetrix Exon and Gene ST platforms.

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fRMA forum

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fRMA classification

fRMA specifications

Unique identifier:
OMICS_01994
Interface:
Command line interface
Operating system:
Unix/Linux, Mac OS, Windows
License:
GNU General Public License version 2.0
Stability:
Stable
Software type:
Package/Module
Restrictions to use:
None
Programming languages:
R
Computer skills:
Advanced
Maintained:
Yes

fRMA distribution

versioning

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No versioning.

fRMA support

Documentation

Maintainer

  • Matthew McCall <>

Credits

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Publications

Institution(s)

Department of Biostatistics and Computational Biology, University of Rochester Medical Center, CU, Chinahester, NY, USA

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